BACKGROUND: Congenital malaria, characterised by low parasitaemia in newborns' peripheral blood, is difficult to diagnose by conventional techniques. Owing to its high sensitivity, polymerase chain reaction (PCR) allows for effective detection of low-density plasmodium infections. This study determined the prevalence of congenital malaria by PCR in newborns of mothers living in a malaria-endemic area of Kinshasa, Democratic Republic of Congo (DRC). METHODS: A total of 576 mother-newborn pairs were enrolled in two clinical trials in Kinshasa. Maternal peripheral blood was collected at enrolment. At delivery, samples were taken from maternal and newborn peripheral blood, placental blood and placental imprints. RESULTS: The prevalence of congenital malaria detected by PCR was 2.4% (14/576) compared with 0.9% (5/576) by microscopy. The prevalence of malaria at delivery was 8.9% (51/570), and placental malaria was 10.6% (59/556) by microscopy. At delivery, maternal malaria was significantly associated with congenital malaria [adjusted odds ratio (aOR) 16.06, 95% CI 2.6-98.5, CONCLUSIONS: Although this first assessment of congenital malaria by PCR in DRC found a low prevalence, maternal and placental malaria at delivery were still associated with congenital malaria, highlighting the importance of maternal health in preventing neonatal infections.